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      Mitochondrial phylogenomics reveals the sister relationship between the endogean Mediterranean raymondionymine weevils and the remaining 51,000+ Curculionidae (Coleoptera)

      , ,
      Arthropod Systematics & Phylogeny
      Pensoft Publishers

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          Abstract

          The tribe Raymondionymini has long been neglected in phylogenetic studies. The tribe is characterized by uncertain monophyly, fluctuating taxonomic status, and a composition prone to instability. All raymondionymine weevils are wingless and have eyes either completely absent or, rarely, consisting of a single ommatidium. With body lengths predominantly below three millimeters, they inhabit deep soil environments and are infrequently collected. The core of this tribe comprises nine genera distributed in Europe and around the Mediterranean region and encompassing 76 species, while six additional genera include 17 species distributed in USA (California), Mexico, Ecuador, Venezuela, Russian Far East, and Madagascar. Here, we present eight new mitogenomes, complemented by one publicly available, encompassing all but two Mediterranean genera of raymondionymine weevils. We used publicly available Curculionoidea mitogenomes to compile an all-inclusive dataset with 391 terminals and a reduced dataset with 61 terminals representing main families of Curculionoidea and subfamilies within Curculionidae. Our maximum likelihood and Bayesian phylogenetic analyses, employing both DNA and amino acids datasets under alternative partition schemes, consistently produced congruent phylogenies. Our results show that the Mediterranean raymondionymines form a strongly supported clade, and their easternmost and morphologically distinct genus Ubychia is sister to the rest of them. Most notably, our results consistently recover a sister relationship between the clade of Mediterranean raymondionymine weevils and a clade encompassing all remaining Curculionidae. Consequently, we propose a revision of weevil taxonomy: (i) Our target group is removed from the non-monophyletic subfamily Brachycerinae; (ii) this clade is resurrected to its former subfamily level within Curculionidae, as the subfamily Raymondionyminae stat. rev; (iii) the nine Mediterranean genera Alaocephala, Alaocyba, Coiffaitiella, Derosasius, Ferreria, Raymondiellus, Raymondionymus, Tarattostichus, and Ubychia compose Raymondionyminae stat. rev; (iv) and non-Mediterranean genera Alaocybites, Bordoniola, Gilbertiola, Homosomus, Neoubychia, and Schizomicrus are considered as “incertae sedis” pending further phylogenetic corroboration. We hypothesize that the remaining Brachycerinae and the non-Mediterranean representatives within Raymondionyminae constitute a series of species-poor early-diverging lineages representing currently unrecognized subfamilies of Curculionidae.

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          Trimmomatic: a flexible trimmer for Illumina sequence data

          Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
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            Basic local alignment search tool.

            A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.
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              Is Open Access

              RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

              Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.

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                Contributors
                (View ORCID Profile)
                Journal
                Arthropod Systematics & Phylogeny
                ASP
                Pensoft Publishers
                1864-8312
                1863-7221
                September 19 2024
                September 19 2024
                : 82
                : 607-620
                Article
                10.3897/asp.82.e112684
                f0bb7308-d49a-4364-bc1f-4f328a29f2eb
                © 2024

                https://creativecommons.org/share-your-work/public-domain/cc0/

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